DNA of microorganisms extracted from diverse, as-received bentonite clays and enrichment cultures.

Characterizing the microbiology of bentonite clays can help with predicting the long-term stability of nuclear fuel waste because such swelling clays represent an important component of most proposed engineered barrier system designs for deep geological repositories. Although cultivation-based quantification of microbial populations from bentonite clays is commonplace, nucleic acid detection of microorganisms in these materials has been difficult due to technical challenges previously associated with extraction and detection of nucleic acids from clays. Because circumventing such challenges enables direct comparisons of cultivation and high-throughput sequencing approaches, we compared results from these approaches using the same 15 bentonite clay reference samples. In all cases, microbial profiles generated by sequencing of nucleic acids extracted from clay detected a larger number of ASVs compared than those generated by cultivation approaches. Despite distinct bentonite clay 16S rRNA gene profiles originating from location- and batch-specific clays, the corresponding profiles from cultures revealed highly similar cultured sulfate-reducing bacteria, denitrifiers, aerobic heterotrophs, and fermenters. Few core taxa were shared among datasets compared here, yet those that did overlap were affiliated with Streptomyces, Micrococcaceae, Bacillus, and Desulfosporosinus. These putative desiccation-resistant bacteria may thus serve as useful targets for experiments that evaluate microbial viability and growth within future pressure-cell experiments, given that our data confirm their consistent viability and substantial relative abundance across diverse bentonite clay samples.